title: Stability of RNA hairpins closed by wobble base pairs.
abstract: Thermodynamic parameters are reported for hairpin formation in 1 M NaCl by RNA sequences of the type GGXANmAYCC, where XY is the wobble base pair, GU or UG, and the underlined loop sequences are three to eight nucleotides. A nearest-neighbor analysis indicates the free energy of loop formation is dependent upon loop size and closing base pair. Hairpin loops closed by UG base pairs are on average 1.3 kcal/mol less stable than hairpins closed by GU base pairs. The hairpin loops closed by UG have approximately the same stability as hairpin loops closed by AU/UA base pairs, while the loops closed by GU are approximately 0.7 kcal/mol more stable than hairpins loops closed by GC/CG base pairs. These results, combined with the model previously developed [Serra et al. (1997) Biochemistry 36, 4844] to predict the stability for hairpin loops closed by Watson-Crick base pairs, allow for the following model to predict the stability of hairpin loops: delta G degree 37L(n) = delta G degree 37iL(n) + delta G degree 37mm + 0.6 (if closed by AU, UA, or UB) - 0.7 (if closed by GU) - 0.7 (if first mismatch is GA or UU except for loops closed by GU). Here, delta G degree 37iL(n) is the free energy increment for initiating a loop of n nucleotides with a CG or GC pair, and delta G degree 37mm is the free energy for the interaction of the first mismatch with the closing base pair. For hairpin loops of n = 4-9, delta G037iL(n) is 4.9, 5.0, 5.0, 5.0, 4.9, and 5.5 kcal/mol, respectively. For hairpin loops of n = 3, delta G degree 37L(3) = +4.8 + 0.6 (if closed by AU, UA, or UG) kcal/mol. Thermodynamic parameters for hairpin formation in 1 M NaCl for 13 naturally occurring RNA hairpin sequences closed by wobble base pairs are reported. The model provides good agreement for both TM and delta G degree 37 for most hairpins studied. Thermodynamic values for five terminal mismatches adjacent to wobble base pairs are also reported.
authors.affiliation: Department of Chemistry, Allegheny College, Meadville, Pennsylvania 16335, USA.
authors.forename: M R
authors.initials: MR
authors.lastname: Giese
authors.forename: K
authors.initials: K
authors.lastname: Betschart
authors.forename: T
authors.initials: T
authors.lastname: Dale
authors.forename: C K
authors.initials: CK
authors.lastname: Riley
authors.forename: C
authors.initials: C
authors.lastname: Rowan
authors.forename: K J
authors.initials: KJ
authors.lastname: Sprouse
authors.forename: M J
authors.initials: MJ
authors.lastname: Serra
mesh_terms: D001482:Base Composition; D005815:Genetic Code; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009843:Oligoribonucleotides / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D009843:Oligoribonucleotides; D012313:RNA